Long-read assemblies reveal structural diversity in genomes of organelles - an example with Acacia pycnantha

Anna E Syme; Todd G B McLay; Frank Udovicic; David J Cantrill; Daniel J Murphy

doi:10.46471/gigabyte.36

Long-read assemblies reveal structural diversity in genomes of organelles - an example with Acacia pycnantha

GigaByte. 2021 Dec 20:2021:gigabyte36. doi: 10.46471/gigabyte.36. eCollection 2021.

Authors

Anna E Syme^{1

2}, Todd G B McLay^{1

3

4}, Frank Udovicic¹, David J Cantrill¹, Daniel J Murphy¹

Affiliations

¹ Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne 3004, Australia.
² Melbourne Bioinformatics, The University of Melbourne, Parkville 3010, Australia.
³ School of BioSciences, The University of Melbourne, Parkville 3010, Australia.
⁴ Centre for Australian National Biodiversity Research, CSIRO, GPO Box 1700, Canberra 2601, Australia.

Abstract

Organelle genomes are typically represented as single, static, circular molecules. However, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and assembled chloroplast and mitochondrial genomes of the Golden Wattle, Acacia pycnantha, using long reads, iterative baiting to extract organelle-only reads, and several assembly algorithms to explore genomic structure. Using a de novo assembly approach agnostic to previous hypotheses about structure, we found that different assemblies revealed contrasting arrangements of genomic segments; a hypothesis supported by mapped reads spanning alternate paths.

Grants and funding

This project was funded by the Genomics for Australian Plants Framework Initiative consortium, which is supported by funding from Bioplatforms Australia (enabled by the Australian National Collaborative Research Infrastructure Strategy), the Ian Potter Foundation, Royal Botanic Gardens Victoria, the Royal Botanic Gardens and Domain Trust, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Centre for Australian National Biodiversity Research and the Department of Biodiversity, Conservation and Attractions, Western Australia.